Dave is correct there are two watertight hatches in the fin (in the RN it is always called a fin not a conning tower). If the weather was really rough then one of the hatches would be shut. The snort ventilation system could then be lined up to provide ventilation and air into the pressure hull as well as to run diesals.

Shutting one of the fin hatches was a decision to be made by the skipper. If the boat had to perform a crash dive then it would take time (valuable seconds) to open the hatch, drop through and secure it.

If a freak wave did poop the fin then the deluge down below would be such that no splashguards would fully protect the panels in the control room below.

One of our Superb class boats was knocked sideways by a freak wave whilst on the surface in the Atlantic in the late 70's, one crewman was lost and the boat nearly did not right itself. By all accounts it was a terrifying experience.

An added danger would be if sea water had reached the main battery compartment. The sea water pouring over the battery would cause an electolytic reaction generating chlorine. Thankfully this did not happen or else the entire crew could have been gassed.

There are also other hatches on the Upholder class. Two forward, the torpedo loading hatch and fwd escape tower, also a main access hatch, aft there would be the aft escape hatch. Once the boat leaves harbour these would be shut and clipped as the casing would be awash most of the time. Up until the casing is secured for sea the surface speed would be kept down to prevent the casing being overwashed.

Any links to the enquiry results?

While I was in boats I knew people who were serving on the Upholder class and they often spoke of design problems.